## ----setup, include = FALSE----------------------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) options(width=100) ## ----getPackage, eval=FALSE----------------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("Rhisat2") ## ---- eval = FALSE-------------------------------------------------------------------------------- # BiocManager::install("fmicompbio/Rhisat2") ## ------------------------------------------------------------------------------------------------- library(Rhisat2) ## ------------------------------------------------------------------------------------------------- list.files(system.file("extdata/refs", package="Rhisat2"), pattern="\\.fa$") refs <- list.files(system.file("extdata/refs", package="Rhisat2"), full.names=TRUE, pattern="\\.fa$") td <- tempdir() hisat2_build(references=refs, outdir=td, prefix="myindex", force=TRUE, strict=TRUE, execute=TRUE) ## ------------------------------------------------------------------------------------------------- print(hisat2_build(references=refs, outdir=td, prefix="myindex", force=TRUE, strict=TRUE, execute=FALSE)) ## ------------------------------------------------------------------------------------------------- list.files(system.file("extdata/reads", package="Rhisat2"), pattern="\\.fastq$") reads <- list.files(system.file("extdata/reads", package="Rhisat2"), pattern="\\.fastq$", full.names=TRUE) hisat2(sequences=as.list(reads), index=file.path(td, "myindex"), type="paired", outfile=file.path(td, "out.sam"), force=TRUE, strict=TRUE, execute=TRUE) ## ------------------------------------------------------------------------------------------------- spsfile <- tempfile() gtf <- system.file("extdata/refs/genes.gtf", package="Rhisat2") extract_splice_sites(features=gtf, outfile=spsfile) hisat2(sequences=as.list(reads), index=file.path(td, "myindex"), type="paired", outfile=file.path(td, "out_sps.sam"), `known-splicesite-infile`=spsfile, force=TRUE, strict=TRUE, execute=TRUE) ## ------------------------------------------------------------------------------------------------- hisat2_version() ## ------------------------------------------------------------------------------------------------- hisat2_build_usage() ## ------------------------------------------------------------------------------------------------- hisat2_usage() ## ------------------------------------------------------------------------------------------------- sessionInfo()